BioMCP is an MCP server that gives LLMs access to 40+ biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, structures, patents, and genomics.
Gene tools: search, detailed section-based fetch, associated diseases/drugs/trials/articles, and pathway enrichment.
Variant tools: search by rsID/HGVS/gene/ClinVar, detailed annotations (frequency/predictions/clinical), OncoKB cancer annotations, and variant-specific trials.
Drug & disease tools: search and detailed retrieval, drug-target and drug-disease associations, and clinical trial lookups.
Literature tools: federated article search across PubMed, EuropePMC, Semantic Scholar, PubTator, and LitSense, plus article details with open-access, annotations, citation graphs, and fast/full citation data.
Clinical trials: search with status/phase/intervention filters and cursor pagination; detailed trial info with eligibility, locations, and outcomes.
Utility tools: free-text concept resolution (discover) and parallel multi-entity retrieval (batch_get).
Structural biology: search PDB, fetch entry metadata (polymer entities, ligands, assembly, experiment, citation), and download mmCIF/PDB files.
Patents: worldwide search with assignee/inventor/CPC/status/date filters and relevance ranking; details with abstract, claims, citations, family, and classifications.
Functional genomics & sequences: GEO series/sample search and SOFT records, SRA experiment/run/study/sample metadata, GenBank/RefSeq fetch with region slicing and NCBI Gene mapping, and GTEx v10 expression and cis-eQTLs.
Ensembl tools: gene lookup across 356 species, orthologue/paralogue search, VEP variant consequence prediction, and genomic region queries.
Optional analysis tools: WebAssembly R differential expression (DESeq2/edgeR/limma), samtools/bedtools/bcftools analysis for BAM/BED/VCF, read-only database SQL tools, and a biomcp_configure meta-tool for configuration management.
Provides access to biomedical literature through PubMed, enabling search and retrieval of articles, and citation data via the article_search and article_get tools.
Integrates with Semantic Scholar for federated literature search and citation analysis, supporting article search and citation graph data.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@BioMCP get info on BRCA1 gene"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
A high-performance MCP server that gives LLMs access to 40 biomedical tools federated across 50+ upstream APIs — genes, variants, drugs, diseases, literature, clinical trials, structural biology, and functional genomics in a single integration.
41 tools across 15 registration modules — search, retrieve, and cross-reference biomedical entities, plus the biomcp_configure meta tool for configuration observability (+3 optional database tools, +4 optional R analysis tools, +8 optional biowasm analysis tools)
50+ upstream sources — MyGene, MyVariant, MyChem, MyDisease, ClinVar, gnomAD, UniProt, Reactome, OpenTargets, CIViC, OncoKB, DisGeNET, GTEx, STRING, DGIdb, ClinicalTrials.gov, PubMed, EuropePMC, Semantic Scholar, PubTator, LitSense, Monarch Initiative, OpenFDA, NIH Reporter, NCBI GEO, SRA, GenBank, Ensembl, and more
Functional genomics & sequences — GEO series/sample search with SOFT detail parsing, SRA experiment/run metadata, GenBank/RefSeq records with region slices, and GTEx v10 median expression + cis-eQTLs
Section-based fetching — entityGet(id, sections) fans out to multiple sources with per-section timeouts and graceful degradation (failed sections return { _error } instead of crashing)
Federated article search — queries 5 literature backends simultaneously with PMID/PMCID/DOI deduplication
Patent access — worldwide patent search and detail via keyed EPO OPS / USPTO ODP; keyless USPTO Public Search and Google Patents (+Wayback archive) fallbacks
Zero-config startup — works out of the box; optional API keys unlock higher rate limits and premium data
1234 unit tests (mocked, 74 suites) + integration tests across 19 files (live APIs via in-process MCP client, gated skips)
Related MCP server: PubMed Advanced MCP Server
npx biomcp # zero-config stdio MCP server; Node >= 22.13Setup is guided in docs/AGENT-INSTALL.md — copy-paste config snippets for Claude Desktop, Claude Code, Codex, and OpenCode, plus an agent-friendly checklist for API keys and optional features.
Full tool schemas (params, enums, defaults) live in src/server/README.md.
Tool | Description |
| Search genes by symbol, name, or keyword with chromosome filter |
| Get detailed gene info by HGNC symbol with optional sections (core, pathways, protein, ontology, go, interactions, expression, protein_atlas, constraint, druggability, dosage_sensitivity, clinical_evidence, disease_associations, diseases, funding). Set |
| Get diseases associated with a gene (DisGeNET / OpenTargets) |
| Find drugs targeting a gene (OpenTargets) |
| Find clinical trials for a gene |
| Find articles about a gene |
| Pathway enrichment analysis for a gene list (Reactome) |
Tool | Description |
| Search variants by rsid, HGVS, gene, ClinVar significance, frequency, CADD |
| Get detailed variant info with optional sections (frequency, predictions, clinical; |
| Get OncoKB cancer variant annotations (requires |
| Find clinical trials for a variant |
Tool | Description |
| Search drugs by name, mechanism, or keyword |
| Get detailed drug info with optional sections (us_regulatory, eu_regulatory, who_regulatory, safety, targets, indications) |
| Find clinical trials for a drug |
Tool | Description |
| Search diseases by name, phenotype, or keyword |
| Get detailed disease info by ID (DOID, MONDO, OMIM, etc.) with optional sections (gene_associations, phenotypes, pathways) |
| Get drugs for a disease (OpenTargets) |
| Get clinical trials for a disease (ClinicalTrials.gov) |
Tool | Description |
| Federated literature search across PubMed, EuropePMC, Semantic Scholar, PubTator, and LitSense with optional date range filtering |
| Get detailed article info by identifier (PMID, PMCID, or DOI) with optional sections: |
Tool | Description |
| Search clinical trials by condition, intervention, status, or phase. Cursor-based pagination via |
| Get detailed trial info by NCT ID with optional sections (eligibility, locations, outcomes) |
Tool | Description |
| Free-text concept resolution across all entity types |
| Retrieve multiple entities in parallel |
Tool | Description |
| Search PDB structures, get entry metadata with optional sections (polymer entities, ligands, assembly, experiment, citation), and download structure files (mmCIF/PDB) |
Tool | Description |
| Search patents worldwide (US, EP, WO, JP, 100+ authorities) with assignee/inventor/CPC/status/date filters and relevance ranking ( |
| Get patent details by publication number with sections: abstract, claims (US fulltext via USPTO Public Search; EP/WO via EPO OPS), citations (forward + backward), family, classifications |
Tool | Description |
| Search NCBI GEO for functional genomics studies (expression microarrays, RNA-seq, single-cell series) by entry type (GSE/GSM/GPL/GDS) and organism; results carry cross-links (sra_project, bioproject, pubmed_ids) for chaining |
| Get the full SOFT record for a GEO series/sample/platform: summary, organisms, sample preview (≤20), supplementary file URLs, and cross-references; optionally download the first supplementary file |
Tool | Description |
| Search NCBI's Sequence Read Archive for sequencing experiments and runs by free text, accession, or field syntax; returns experiment/study/sample accessions with library strategy and run counts |
| Get full details for an SRA accession: SRR run (instrument, spots, bases, size), SRX experiment (library design), SRP study (experiment list), or SRS sample; ENA/DDBJ accessions rejected with an ENA pointer |
Tool | Description |
| Search NCBI nucleotide records (GenBank/RefSeq/INSDC) by plain terms, accession, or field syntax; results include accession.version, definition, length, organism, topology |
| Fetch a GenBank/RefSeq record as GenBank flat file or FASTA; whole records capped at 2 Mb — larger records require a |
| Map a GenBank/RefSeq accession to its NCBI Gene IDs (elink nuccore→gene) for bridging into gene tools |
Tool | Description |
| Get median gene expression across GTEx tissues (Analysis v10, 54 tissue sites, TPM, highest first); accepts HGNC symbol or Ensembl gene ID, with optional single-tissue filter |
| Get significant cis-eQTL associations for a gene in a specific GTEx tissue (v10): variant_id, p_value, NES, slope, sorted by ascending p-value |
Tool | Description |
| Resolve a gene in Ensembl terms for any of ~356 species: stable ID (+version), symbol, coordinates on the current assembly, canonical transcript; |
| Find orthologues/paralogues across species via Ensembl Compara — target stable IDs, taxonomy level, percent identity, sorted by identity; filter with |
| Compute variant consequences on demand via Ensembl VEP for NOVEL variants and non-human species: most severe consequence, per-transcript effects (SIFT/PolyPhen), co-located ClinVar/COSMIC/gnomAD data. Known human variants get deeper pre-computed scores via |
| Query genes/transcripts/known variants in a genomic interval ( |
ANALYSIS_R=1)Tool | Description |
| Differential expression for RNA-seq counts with Bioconductor DESeq2 (negative binomial, independent filtering, optional LFC shrinkage) in sandboxed WebAssembly R. Inputs: integer count matrix + sample metadata + design formula; output: markdown table of top genes by adjusted p-value with summary ( |
| Differential expression with edgeR — TMM normalization, empirical-Bayes dispersion, quasi-likelihood F-test ( |
| Differential expression with limma-voom — precision-weighted linear models with empirical-Bayes moderation; same input/output contract |
| R runtime report: R/webR versions, installed package versions, memory, mirror endpoint — for diagnosing analysis issues |
First use starts a ~1 GB WebAssembly R worker and downloads the wasm package bundle (~62 MB) from GitHub releases (cached). Requires webr installed next to biomcp. Guide: docs/R-ANALYSIS.md.
ANALYSIS_BIOWASM=1)Tool | Description |
| Inspect an alignment (SAM/BAM/CRAM): header contigs, sample/read groups, flagstat mapping metrics, per-contig counts via idxstats when indexed — "what's in this BAM?" before region work |
| Reads, depth, pileup, or read extraction in a genomic region (samtools view/depth/mpileup); indexed sources use fast positional retrieval, indexless sources stream a BED filter (depth requires coordinate-sorted input and detects order violations), returning counts, coverage tables, SAM rows, or a BAM artifact |
| Inspect a VCF/BCF: contigs, sample count and names, INFO/FORMAT field inventory from the header |
| Variants in a region as a narrow field projection (bcftools query): chosen columns, sample subsets, expression filters, variant types — or a sliced VCF.gz artifact |
| Interval algebra on BED tracks (bedtools intersect/merge/subtract/coverage/jaccard/sort) with the streaming |
| Format plumbing: SAM/BAM/CRAM via samtools view, VCF/BCF via bcftools view, VCF/BCF → TSV via bcftools query; results are artifact handles reusable as |
| Biowasm runtime report: pinned tool versions, asset cache state, engine status, retained artifacts, memory |
| Constrained escape hatch: an allowlisted samtools/bedtools/bcftools subcommand with schema-validated args (no shell, paths under /shared only) |
First use downloads checksum-verified wasm assets (~4.5 MB, cached); no extra npm packages. Indexed sources answer region queries with fast positional retrieval (~0.2 % of file read); indexless sources fall back to streaming BED filters. Guide: docs/BIOWASM-ANALYSIS.md.
Citations federate 5 providers in fast (~4s) or full (~15-30s) mode. Forward citation lists come from Europe PMC, OpenCitations, and Semantic Scholar; Crossref supplies counts and backward references. Provider matrix and schema details: src/server/README.md.
Capabilities that ship with the package but stay inactive until enabled. Each links to its own guide:
Feature | Enable | Guide |
Database access — read-only SQL tools ( | Set | |
R analysis — Bioconductor differential expression ( | Set | |
Biowasm analysis — samtools/bedtools/bcftools (BAM/BED/VCF) in sandboxed WebAssembly; streams/indexes real human-scale datasets (~300 MB BAM scans, region queries touch ~0.2 % of the file); assets ~4.5 MB cached at first use; no extra npm packages | Set |
Instead of hand-editing env blocks, agents (and users) can self-serve through the always-available biomcp_configure tool: it reports every parameter's status/provenance, writes the .biomcp.json project config file for the optional features above (env vars keep precedence; env-only parameters are query-only and value-masked), validates changes, detects conflicts, checks peer-dependency prerequisites, and spells out the restart/verify steps. Details: docs/ENV-VARS.md → Project config file.
Doc | Contents |
Guided installation & client configuration (Claude Desktop, Claude Code, Codex, OpenCode) | |
Single source of truth for every environment variable | |
Database access feature guide | |
R analysis feature guide (Bioconductor in WebAssembly) | |
Biowasm analysis feature guide (samtools/bedtools/bcftools in WebAssembly) | |
Build, test, publish workflow | |
CI pipeline, Dependabot automation, auto-merge safety model | |
Full tool schemas (params, enums, defaults) | |
User-agent E2E tests for the analysis tools |
Licensed under the Apache License, Version 2.0. See NOTICE for attributions.
BioMCP-TS is adapted from the upstream BioMCP Rust project (MIT) with an agent-first development approach and enhancements — kudos to the original authors.
Unclaimed servers have limited discoverability.
If you are the server author, to access and configure the admin panel.
MCP gateway federating 21 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP.
Auditable MCP server for PubMed, Europe PMC, ClinicalTrials.gov, and bioRxiv/medRxiv queries
AI Reasoning Cache & Consensus Layer with 11 MCP tools via Streamable HTTP.
We provide all the information about MCP servers via our MCP API.
curl -X GET 'https://glama.ai/api/mcp/v1/servers/yeyuan98/biomcp-ts'
If you have feedback or need assistance with the MCP directory API, please join our Discord server
